OpenRaiser/Intern-Atlas huggingface dataset:
Information-Theoretic Foundations of DNA Data Storage
Venue: arXiv cs.IT 2022
Year: 2022

Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental storage systems, making it a promising solution for our society's increasing need of data storage. While in living things, DNA molecules can consist of millions of nucleotides, due to technological constraints, in practice, data is stored on many short DNA molecules, which are preserved in a DNA pool and cannot be spatially ordered. Moreover, imperfections in sequencing, synthesis, and handling, as well as DNA decay during storage, introduce random noise into the system, making the task of reliably storing and retrieving information in DNA challenging. This unique setup raises a natural information-theoretic question: how much information can be reliably stored on and reconstructed from millions of short noisy sequences? The goal of this monograph is to address this question by discussing the fundamental limits of storing information on DNA. Motivated by current technological constraints on DNA synthesis and sequencing, we propose a probabilistic channel model that captures three key distinctive aspects of the DNA storage systems: (1) the data is written onto many short DNA molecules that are stored in an unordered fashion; (2) the molecules are corrupted by noise and (3) the data is read by randomly sampling from the DNA pool. Our goal is to investigate the impact of each of these key aspects on the capacity of the DNA storage system. Rather than focusing on coding-theoretic considerations and computationally efficient encoding and decoding, we aim to build an information-theoretic foundation for the analysis of these channels, developing tools for achievability and converse arguments.
Real time A* Adaptive Action Set Footstep Planning with Human Locomotion Energy Approximations Considering Angle Difference for Heuristic Function
Venue: arXiv cs.RO 2022
Year: 2022

The problem of navigating a bipedal robot to a desired destination in various environments is very important. However, it is very difficult to solve the navigation problem in real time because the computation time is very long due to the nature of the biped robot having a high degree of freedom. In order to overcome this, many scientists suggested navigation through the footstep planning. Usually footstep planning use the shortest distance or angles as the objective function based on the A * algorithm. Recently, the energy required for human walking, which is widely used in human dynamics, approximated by a polynomial function is proposed as a better cost function that explains the movement of the bipedal robot. In addition, for the real time navigation, using the action set of the A * algorithm not fixed, but the number changing according to the situation, so that the computation time does not increase much and the methods of considering the collision with the external environment are suggested as a practical method. In this thesis, polynomial function approximating the energy required for human walking is adopted as a cost function, and heuristic function considering the angular difference between the robot and the destination which is not shown in the previous studies is newly proposed and proved. In addition, a new method to integrate the adaptive behavior set and energy related to human walking is proposed. Furthermore, efficient collision avoidance method and a method to reduce the local minimum problem is proposed in this framework. Finally, footstep planning algorithm with all of these features into the mapping algorithm and the walking algorithm to solve the navigation problem is validated with simulation and real robot.
Hyperbolic Cosine Transformer for LiDAR 3D Object Detection
Venue: arXiv cs.CV 2022
Year: 2022

Recently, Transformer has achieved great success in computer vision. However, it is constrained because the spatial and temporal complexity grows quadratically with the number of large points in 3D object detection applications. Previous point-wise methods are suffering from time consumption and limited receptive fields to capture information among points. In this paper, we propose a two-stage hyperbolic cosine transformer (ChTR3D) for 3D object detection from LiDAR point clouds. The proposed ChTR3D refines proposals by applying cosh-attention in linear computation complexity to encode rich contextual relationships among points. The cosh-attention module reduces the space and time complexity of the attention operation. The traditional softmax operation is replaced by non-negative ReLU activation and hyperbolic-cosine-based operator with re-weighting mechanism. Extensive experiments on the widely used KITTI dataset demonstrate that, compared with vanilla attention, the cosh-attention significantly improves the inference speed with competitive performance. Experiment results show that, among two-stage state-of-the-art methods using point-level features, the proposed ChTR3D is the fastest one.
Exploring Robustness of Prefix Tuning in Noisy Data: A Case Study in Financial Sentiment Analysis
Venue: arXiv cs.CL 2022
Year: 2022

The invention of transformer-based models such as BERT, GPT, and RoBERTa has enabled researchers and financial companies to finetune these powerful models and use them in different downstream tasks to achieve state-of-the-art performance. Recently, a lightweight alternative (approximately 0.1% - 3% of the original model parameters) to fine-tuning, known as prefix tuning has been introduced. This method freezes the model parameters and only updates the prefix to achieve performance comparable to full fine-tuning. Prefix tuning enables researchers and financial practitioners to achieve similar results with much fewer parameters. In this paper, we explore the robustness of prefix tuning when facing noisy data. Our experiments demonstrate that fine-tuning is more robust to noise than prefix tuning -- the latter method faces a significant decrease in performance on most corrupted data sets with increasing noise levels. Furthermore, prefix tuning has high variances in the F1 scores compared to fine-tuning in many corruption methods. We strongly advocate that caution should be carefully taken when applying the state-of-the-art prefix tuning method to noisy data.
Prompt Learning for Domain Adaptation in Task-Oriented Dialogue
Venue: arXiv cs.CL 2022
Year: 2022

Conversation designers continue to face significant obstacles when creating production quality task-oriented dialogue systems. The complexity and cost involved in schema development and data collection is often a major barrier for such designers, limiting their ability to create natural, user-friendly experiences. We frame the classification of user intent as the generation of a canonical form, a lightweight semantic representation using natural language. We show that canonical forms offer a promising alternative to traditional methods for intent classification. By tuning soft prompts for a frozen large language model, we show that canonical forms generalize very well to new, unseen domains in a zero- or few-shot setting. The method is also sample-efficient, reducing the complexity and effort of developing new task-oriented dialogue domains.
Perfectly predicting ICU length of stay: too good to be true
Venue: arXiv cs.LG 2022
Year: 2022

A paper of Alsinglawi et al was recently accepted and published in Scientific Reports. In this paper, the authors aim to predict length of stay (LOS), discretized into either long (> 7 days) or short stays (< 7 days), of lung cancer patients in an ICU department using various machine learning techniques. The authors claim to achieve perfect results with an Area Under the Receiver Operating Characteristic curve (AUROC) of 100% with a Random Forest (RF) classifier with ADASYN class balancing over sampling technique, which if accurate could have significant implications for hospital management. However, we have identified several methodological flaws within the manuscript which cause the results to be overly optimistic and would have serious consequences if used in a clinical practice. Moreover, the reporting of the methodology is unclear and many important details are missing from the manuscript, which makes reproduction extremely difficult. We highlight the effect these oversights have had on the result and provide a more believable result of 88.91% AUROC when these oversights are corrected.
Warmup and Transfer Knowledge-Based Federated Learning Approach for IoT Continuous Authentication
Venue: arXiv cs.LG 2022
Year: 2022

Continuous behavioural authentication methods add a unique layer of security by allowing individuals to verify their unique identity when accessing a device. Maintaining session authenticity is now feasible by monitoring users' behaviour while interacting with a mobile or Internet of Things (IoT) device, making credential theft and session hijacking ineffective. Such a technique is made possible by integrating the power of artificial intelligence and Machine Learning (ML). Most of the literature focuses on training machine learning for the user by transmitting their data to an external server, subject to private user data exposure to threats. In this paper, we propose a novel Federated Learning (FL) approach that protects the anonymity of user data and maintains the security of his data. We present a warmup approach that provides a significant accuracy increase. In addition, we leverage the transfer learning technique based on feature extraction to boost the models' performance. Our extensive experiments based on four datasets: MNIST, FEMNIST, CIFAR-10 and UMDAA-02-FD, show a significant increase in user authentication accuracy while maintaining user privacy and data security.
BERT in Plutarch's Shadows
Venue: arXiv cs.CL 2022
Year: 2022

The extensive surviving corpus of the ancient scholar Plutarch of Chaeronea (ca. 45-120 CE) also contains several texts which, according to current scholarly opinion, did not originate with him and are therefore attributed to an anonymous author Pseudo-Plutarch. These include, in particular, the work Placita Philosophorum (Quotations and Opinions of the Ancient Philosophers), which is extremely important for the history of ancient philosophy. Little is known about the identity of that anonymous author and its relation to other authors from the same period. This paper presents a BERT language model for Ancient Greek. The model discovers previously unknown statistical properties relevant to these literary, philosophical, and historical problems and can shed new light on this authorship question. In particular, the Placita Philosophorum, together with one of the other Pseudo-Plutarch texts, shows similarities with the texts written by authors from an Alexandrian context (2nd/3rd century CE).
FedLesScan: Mitigating Stragglers in Serverless Federated Learning
Venue: arXiv cs.DC 2022
Year: 2022

Federated Learning (FL) is a machine learning paradigm that enables the training of a shared global model across distributed clients while keeping the training data local. While most prior work on designing systems for FL has focused on using stateful always running components, recent work has shown that components in an FL system can greatly benefit from the usage of serverless computing and Function-as-a-Service technologies. To this end, distributed training of models with serverless FL systems can be more resource-efficient and cheaper than conventional FL systems. However, serverless FL systems still suffer from the presence of stragglers, i.e., slow clients due to their resource and statistical heterogeneity. While several strategies have been proposed for mitigating stragglers in FL, most methodologies do not account for the particular characteristics of serverless environments, i.e., cold-starts, performance variations, and the ephemeral stateless nature of the function instances. Towards this, we propose FedLesScan, a novel clustering-based semi-asynchronous training strategy, specifically tailored for serverless FL. FedLesScan dynamically adapts to the behaviour of clients and minimizes the effect of stragglers on the overall system. We implement our strategy by extending an open-source serverless FL system called FedLess. Moreover, we comprehensively evaluate our strategy using the 2nd generation Google Cloud Functions with four datasets and varying percentages of stragglers. Results from our experiments show that compared to other approaches FedLesScan reduces training time and cost by an average of 8% and 20% respectively while utilizing clients better with an average increase in the effective update ratio of 17.75%.
The CRINGE Loss: Learning what language not to model
Venue: arXiv cs.CL 2022
Year: 2022

Standard language model training employs gold human documents or human-human interaction data, and treats all training data as positive examples. Growing evidence shows that even with very large amounts of positive training data, issues remain that can be alleviated with relatively small amounts of negative data -- examples of what the model should not do. In this work, we propose a novel procedure to train with such data called the CRINGE loss (ContRastive Iterative Negative GEneration). We show the effectiveness of this approach across three different experiments on the tasks of safe generation, contradiction avoidance, and open-domain dialogue. Our models outperform multiple strong baselines and are conceptually simple, easy to train and implement.
DHT-based Edge and Fog Computing Systems: Infrastructures and Applications
Venue: arXiv cs.DC 2022
Year: 2022

Intending to support new emerging applications with latency requirements below what can be offered by the cloud data centers, the edge and fog computing paradigms have reared. In such systems, the real-time instant data is processed closer to the edge of the network, instead of the remote data centers. With the advances in edge and fog computing systems, novel and efficient solutions based on Distributed Hash Tables (DHTs) emerge and play critical roles in system design. Several DHT-based solutions have been proposed to either augment the scalability and efficiency of edge and fog computing infrastructures or to enable application-specific functionalities such as task and resource management. This paper presents the first comprehensive study on the state-of-the-art DHT-based architectures in edge and fog computing systems from the lenses of infrastructure and application. Moreover, the paper details the open problems and discusses future research guidelines for the DHT-based edge and fog computing systems.
Colocating Real-time Storage and Processing: An Analysis of Pull-based versus Push-based Streaming
Venue: arXiv cs.DC 2022
Year: 2022

Real-time Big Data architectures evolved into specialized layers for handling data streams' ingestion, storage, and processing over the past decade. Layered streaming architectures integrate pull-based read and push-based write RPC mechanisms implemented by stream ingestion/storage systems. In addition, stream processing engines expose source/sink interfaces, allowing them to decouple these systems easily. However, open-source streaming engines leverage workflow sources implemented through a pull-based approach, continuously issuing read RPCs towards the stream ingestion/storage, effectively competing with write RPCs. This paper proposes a unified streaming architecture that leverages push-based and/or pull-based source implementations for integrating ingestion/storage and processing engines that can reduce processing latency and increase system read and write throughput while making room for higher ingestion. We implement a novel push-based streaming source by replacing continuous pull-based RPCs with one single RPC and shared memory (storage and processing handle streaming data through pointers to shared objects). To this end, we conduct an experimental analysis of pull-based versus push-based design alternatives of the streaming source reader while considering a set of stream benchmarks and microbenchmarks and discuss the advantages of both approaches.
Switching Attention in Time-Varying Environments via Bayesian Inference of Abstractions
Venue: arXiv cs.RO 2022
Year: 2022

Motivated by the goal of endowing robots with a means for focusing attention in order to operate reliably in complex, uncertain, and time-varying environments, we consider how a robot can (i) determine which portions of its environment to pay attention to at any given point in time, (ii) infer changes in context (e.g., task or environment dynamics), and (iii) switch its attention accordingly. In this work, we tackle these questions by modeling context switches in a time-varying Markov decision process (MDP) framework. We utilize the theory of bisimulation-based state abstractions in order to synthesize mechanisms for paying attention to context-relevant information. We then present an algorithm based on Bayesian inference for detecting changes in the robot's context (task or environment dynamics) as it operates online, and use this to trigger switches between different abstraction-based attention mechanisms. Our approach is demonstrated on two examples: (i) an illustrative discrete-state tracking problem, and (ii) a continuous-state tracking problem implemented on a quadrupedal hardware platform. These examples demonstrate the ability of our approach to detect context switches online and robustly ignore task-irrelevant distractors by paying attention to context-relevant information.
On the Ramifications of Human Label Uncertainty
Venue: arXiv cs.CV 2022
Year: 2022

Humans exhibit disagreement during data labeling. We term this disagreement as human label uncertainty. In this work, we study the ramifications of human label uncertainty (HLU). Our evaluation of existing uncertainty estimation algorithms, with the presence of HLU, indicates the limitations of existing uncertainty metrics and algorithms themselves in response to HLU. Meanwhile, we observe undue effects in predictive uncertainty and generalizability. To mitigate the undue effects, we introduce a novel natural scene statistics (NSS) based label dilution training scheme without requiring massive human labels. Specifically, we first select a subset of samples with low perceptual quality ranked by statistical regularities of images. We then assign separate labels to each sample in this subset to obtain a training set with diluted labels. Our experiments and analysis demonstrate that training with NSS-based label dilution alleviates the undue effects caused by HLU.
A Gait Triaging Toolkit for Overlapping Acoustic Events in Indoor Environments
Venue: arXiv cs.SD 2022
Year: 2022

Gait has been used in clinical and healthcare applications to assess the physical and cognitive health of older adults. Acoustic based gait detection is a promising approach to collect gait data of older adults passively and non-intrusively. However, there has been limited work in developing acoustic based gait detectors that can operate in noisy polyphonic acoustic scenes of homes and care homes. We attribute this to the lack of good quality gait datasets from the real-world to train a gait detector on. In this paper, we put forward a novel machine learning based filter which can triage gait audio samples suitable for training machine learning models for gait detection. The filter achieves this by eliminating noisy samples at an f(1) score of 0.85 and prioritising gait samples with distinct spectral features and minimal noise. To demonstrate the effectiveness of the filter, we train and evaluate a deep learning model on gait datasets collected from older adults with and without applying the filter. The model registers an increase of 25 points in its f(1) score on unseen real-word gait data when trained with the filtered gait samples. The proposed filter will help automate the task of manual annotation of gait samples for training acoustic based gait detection models for older adults in indoor environments.
Multi-domain Cooperative SLAM: The Enabler for Integrated Sensing and Communications
Venue: arXiv cs.IT 2022
Year: 2022

Simultaneous localization and mapping (SLAM) provides user tracking and environmental mapping capabilities, enabling communication systems to gain situational awareness. Advanced communication networks with ultra-wideband, multiple antennas, and a large number of connections present opportunities for deep integration of sensing and communications. First, the development of integrated sensing and communications (ISAC) is reviewed in this study, and the differences between ISAC and traditional communication are revealed. Then, efficient mechanisms for multi-domain collaborative SLAM are presented. In particular, research opportunities and challenges for cross-sensing, cross-user, cross-frequency, and cross-device SLAM mechanisms are proposed. In addition, SLAM-aided communication strategies are explicitly discussed. We prove that the multi-domain cooperative SLAM mechanisms based on hybrid sensing and crowdsourcing can considerably improve the accuracy of localization and mapping in complex multipath propagation environments through numerical analysis. Furthermore, we conduct testbed experiments to show that the proposed SLAM mechanisms can achieve decimeter-level localization and mapping accuracy in practical scenarios, thereby proving the application prospect of multi-domain collaborative SLAM in ISAC.
Does Deep Learning REALLY Outperform Non-deep Machine Learning for Clinical Prediction on Physiological Time Series?
Venue: arXiv cs.LG 2022
Year: 2022

Machine learning has been widely used in healthcare applications to approximate complex models, for clinical diagnosis, prognosis, and treatment. As deep learning has the outstanding ability to extract information from time series, its true capabilities on sparse, irregularly sampled, multivariate, and imbalanced physiological data are not yet fully explored. In this paper, we systematically examine the performance of machine learning models for the clinical prediction task based on the EHR, especially physiological time series. We choose Physionet 2019 challenge public dataset to predict Sepsis outcomes in ICU units. Ten baseline machine learning models are compared, including 3 deep learning methods and 7 non-deep learning methods, commonly used in the clinical prediction domain. Nine evaluation metrics with specific clinical implications are used to assess the performance of models. Besides, we sub-sample training dataset sizes and use learning curve fit to investigate the impact of the training dataset size on the performance of the machine learning models. We also propose the general pre-processing method for the physiology time-series data and use Dice Loss to deal with the dataset imbalanced problem. The results show that deep learning indeed outperforms non-deep learning, but with certain conditions: firstly, evaluating with some particular evaluation metrics (AUROC, AUPRC, Sensitivity, and FNR), but not others; secondly, the training dataset size is large enough (with an estimation of a magnitude of thousands).